A saved search views a subset of an existing library. Using that same saved search as a restriction and the saved search becomes its own virtual library. It is no longer a subset and anything you do is limited to this group. Note the difference in the Tag browser numbers and the total books in the library.

I agree with dwanthny about not messing with separate libraries. If you want a semantic separation from tags, another solution might be a custom column with a set of permitted values. It is presented as a dropdown, and the column will show up in the tag browser. This might be quicker and more flexible than saved searches, as it'll keep your search field free. I made an example for you:

Right click on any column header, and select "Add your own columns" at the bottom. Click the green + sign at the right, enter the values shown in the screenshot, add any other "libraries" you want with commas in between. Restart Calibre (Ctrl+R) and position your column where you want it.

If you want a book to be present in several "libraries", and still have the "library" column be separate from tags, you can use the "Comma separated text, like tags, shown in the tag browser" instead.